RELION Web UI

A browser-based interface for RELION 5 that submits jobs to any Slurm cluster (or runs locally on a single machine). Three deployment shapes cover most cryo-EM setups: no-cluster, plain Slurm, and Open OnDemand.

The user opens the browser, drives a visual pipeline through Import → Motion Correction → CTF → Auto-Pick → Extract → 2D/3D Classification → Refine → Post-Process, and reviews results without touching a command line. Every job runs inside your existing RELION container.

Which deployment shape do I want?

Your situation	Variant	Install command
Single machine, RELION already installed	Local	bash installers/scripts/install_local.sh
Slurm cluster, no Open OnDemand	Headless	sudo bash installers/scripts/install_headless.sh
Slurm cluster with Open OnDemand	OOD	sudo bash installers/scripts/install_ood.sh

All three share the same backend + frontend code; only the installer, service model, and web-server plumbing differ.

Prerequisites

	Local	Headless	OOD
Python 3.10+	✓	✓	✓
RELION 5 container (.sif)	✓ (or native binaries)	✓	✓
Slurm cluster	✗	✓	✓
Open OnDemand 3.x	✗	✗	✓
Root access needed	✗	✓	✓
Shared filesystem across nodes	✗	✓	✓

Quick 3-step recipe (Local variant)

git clone https://github.com/<your-org>/relion-web-ui
cd relion-web-ui
cp examples/env.example relion-web-ui.env
# Edit relion-web-ui.env and set RELION_CONTAINER (or RELION_BIN_PATH)
bash installers/scripts/install_local.sh

Then open http://localhost:5000/ in your browser.

Getting the RELION container

See docs/container.md. Short version: pull the community .sif image, or build your own from RELION's official Dockerfile. Set RELION_CONTAINER=/absolute/path/to/relion.sif in your env file.

Documentation

• docs/quickstart.md - decision tree and one-page install
• docs/install-local.md - full Local install guide
• docs/install-headless.md - full Headless install guide
• docs/install-ood.md - full Open OnDemand install guide
• docs/configuration.md - every env var explained
• docs/container.md - where to get the RELION container
• docs/architecture.md - how the pieces fit together

Architecture at a glance

Browser ── HTTPS ──▶ Flask backend (Python 3.10)
                        │
                        ▼
                    Slurm submission (sbatch / SSH proxy / local subprocess)
                        │
                        ▼
                    Compute node runs RELION inside an Apptainer/Singularity container
                        │
                        ▼
                    Output files land on your shared filesystem
                        │
                        ▼
                    Browser reads results and renders visualizations

Contributing

See CONTRIBUTING.md. Issues and pull requests welcome. No SLA on responses; this is a community project.

Security

See SECURITY.md for the threat model and how to report security issues.

License

Apache License 2.0. See LICENSE.

RELION 5 itself is distributed under its own license (GPL v2). This project is a wrapper that runs RELION as an external subprocess; the two licenses are compatible for the wrapper's intended use.